1UGU Photosynthesis date Jun 19, 2003
title Crystal Structure Of Pyp E46q Mutant
authors M.Sugishima, Y.Tanimoto, N.Hamada, F.Tokunaga, K.Fukuyama
compound source
Molecule: Photoactive Yellow Protein
Chain: A
Synonym: Pyp
Engineered: Yes
Mutation: Yes
Organism_scientific: Halorhodospira Halophila
Organism_taxid: 1053
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet16b
symmetry Space Group: P 65
R_factor 0.165 R_Free 0.191
crystal
cell
length a length b length c angle alpha angle beta angle gamma
40.352 40.352 118.001 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.20 Å
ligand HC4 enzyme
related structures by homologous chain: 1OTD, 1UWN
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructure of photoactive yellow protein (PYP) E46Q mutant at 1.2 A resolution suggests how Glu46 controls the spectroscopic and kinetic characteristics of PYP., Sugishima M, Tanimoto N, Soda K, Hamada N, Tokunaga F, Fukuyama K, Acta Crystallogr D Biol Crystallogr 2004 Dec;60(Pt 12 Pt 2):2305-9. Epub, 2004 Nov 26. PMID:15583378
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (50 Kb) [Save to disk]
  • Biological Unit Coordinates (1ugu.pdb1.gz) 45 Kb
  • LPC: Ligand-Protein Contacts for 1UGU
  • CSU: Contacts of Structural Units for 1UGU
  • Likely Quarternary Molecular Structure file(s) for 1UGU
  • Structure Factors (215 Kb)
  • Retrieve 1UGU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1UGU from S2C, [Save to disk]
  • Re-refined 1ugu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1UGU in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 1UGU
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Conformational Epitope Prediction for 1UGU from the CEP Server.
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1UGU, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ugua_, region A [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1ugu] [1ugu_A]
  • SWISS-PROT database: [P16113]
  • Domain organization of [PYP_HALHA] by SWISSPFAM
  • Domain found in 1UGU: [PAS ] by SMART
  • Other resources with information on 1UGU
  • Community annotation for 1UGU at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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